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Add script to download COVID-19 differential expression data #84

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Sep 21, 2024
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Add script to download COVID-19 differential expression data #84

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: drugfindR
Title: Investigate iLINCS for candidate repurposable drugs
Version: 0.99.986
Version: 0.99.987
Authors@R: c(
person(given = c("Ali", "Sajid"),
family = "Imami",
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4 changes: 2 additions & 2 deletions codemeta.json
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"codeRepository": "https://github.com/CogDisResLab/drugfindR",
"issueTracker": "https://github.com/CogDisResLab/drugfindR/issues",
"license": "https://spdx.org/licenses/GPL-3.0",
"version": "0.99.986",
"version": "0.99.987",
"programmingLanguage": {
"@type": "ComputerLanguage",
"name": "R",
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"applicationCategory": "Genomics",
"isPartOf": "https://bioconductor.org",
"keywords": ["LINCS", "iLINCS", "drugrepurposing", "drugdiscovery", "transcriptomics", "geneexpression", "geneknockdown", "geneoverexpression", "chemicalperturbagen", "drugfindR", "r", "ilincs", "bioinformatics", "bioinformatics-pipeline"],
"fileSize": "2085.479KB",
"fileSize": "2086.498KB",
"releaseNotes": "https://github.com/CogDisResLab/drugfindR/blob/master/NEWS.md",
"readme": "https://github.com/CogDisResLab/drugfindR/blob/devel/README.md",
"contIntegration": ["https://github.com/CogDisResLab/drugfindR/actions/workflows/rworkflows.yml", "https://app.codecov.io/gh/CogDisResLab/drugfindR?branch=devel"],
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19 changes: 19 additions & 0 deletions inst/script/dCovid_diffexp.R
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# This script servers as both documentation and script to downlaod
# the data file dCovid_diffexp.tsv from Zenodo.
#
# This file is used in the vignette to demonstrate the use of the
# drugfindR package.

# The file that we download is part of a set of differential gene expression
# files that are located in the Zenodo repository at the following URL:
# https://zenodo.org/record/10265182
# These files were generated by the author, who is also the author of the
# publication "Identification of candidate repurposable drugs to combat COVID‑19 using a signature‑based approach" (https://doi.org/10.1038/s41598-021-84044-9).
#
# This particular file contains the differential gene expression data for the
# patients with COVID-19 compared to the healthy controls.
url <- "https://zenodo.org/records/10265182/files/dCovid_diffexp.tsv"

# We download the file to the inst/extdata directory of the package.
location <- file.path("inst", "extdata", "dCovid_diffexp.tsv")
download.file(url, location, method = "auto")
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